FMO DATABASE

FMODB ID: K96V3

Calculation Name: 3D7C-A-Xray372

Preferred Name: Histone acetyltransferase GCN5

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3D7C

Chain ID: A

ChEMBL ID: CHEMBL5501

UniProt ID: Q92830

Base Structure: X-ray

Registration Date: 2023-09-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptAll
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	111
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-957813.263105
FMO2-HF: Nuclear repulsion	911166.183664
FMO2-HF: Total energy	-46647.079441
FMO2-MP2: Total energy	-46781.435184

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:727:MET)

Summations of interaction energy for fragment #1(A:727:MET)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-4.434	-7.655	21.016	-1.011	-16.784	-0.027

Interaction energy analysis for fragmet #1(A:727:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.104 / q_NPA : -0.045

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	729	ASP	-1	-0.841	-0.900	2.544	0.128	2.460	0.420	-1.107	-1.646	-0.001
4	A	730	PRO	0	0.017	-0.021	2.271	0.985	0.363	10.978	-5.015	-5.341	-0.003
5	A	731	ASP	-1	-0.798	-0.892	3.039	8.470	2.185	-0.144	7.230	-0.802	-0.006
6	A	732	GLN	0	-0.027	0.008	5.418	0.224	0.224	0.000	0.000	0.000	0.000
7	A	733	LEU	0	-0.009	0.008	2.424	-1.832	-1.865	4.136	-1.013	-3.090	0.005
8	A	734	TYR	0	-0.012	-0.004	4.794	-1.106	-0.980	-0.001	-0.029	-0.096	0.000
9	A	735	THR	0	-0.038	-0.049	6.748	-0.748	-0.748	0.000	0.000	0.000	0.000
10	A	736	THR	0	0.000	-0.003	8.060	-0.392	-0.392	0.000	0.000	0.000	0.000
11	A	737	LEU	0	-0.019	-0.021	6.646	-0.312	-0.312	0.000	0.000	0.000	0.000
12	A	738	LYS	1	0.955	0.981	9.969	-1.118	-1.118	0.000	0.000	0.000	0.000
13	A	739	ASN	0	-0.008	-0.016	12.376	-0.186	-0.186	0.000	0.000	0.000	0.000
14	A	740	LEU	0	-0.001	0.024	12.125	-0.125	-0.125	0.000	0.000	0.000	0.000
15	A	741	LEU	0	0.015	-0.001	13.876	-0.112	-0.112	0.000	0.000	0.000	0.000
16	A	742	ALA	0	-0.018	-0.007	15.698	-0.095	-0.095	0.000	0.000	0.000	0.000
17	A	743	GLN	0	0.008	0.007	17.076	-0.114	-0.114	0.000	0.000	0.000	0.000
18	A	744	ILE	0	-0.010	-0.008	16.274	-0.047	-0.047	0.000	0.000	0.000	0.000
19	A	745	LYS	1	0.856	0.911	18.350	-0.461	-0.461	0.000	0.000	0.000	0.000
20	A	746	SER	0	-0.021	-0.007	21.504	-0.040	-0.040	0.000	0.000	0.000	0.000
21	A	747	HIS	0	-0.001	0.015	23.599	-0.026	-0.026	0.000	0.000	0.000	0.000
22	A	748	PRO	0	0.035	0.014	25.302	-0.005	-0.005	0.000	0.000	0.000	0.000
23	A	749	SER	0	-0.002	-0.008	27.377	-0.013	-0.013	0.000	0.000	0.000	0.000
24	A	750	ALA	0	0.017	0.000	23.752	-0.001	-0.001	0.000	0.000	0.000	0.000
25	A	751	TRP	0	0.007	0.004	25.522	0.000	0.000	0.000	0.000	0.000	0.000
26	A	752	PRO	0	0.007	0.012	27.866	-0.005	-0.005	0.000	0.000	0.000	0.000
27	A	753	PHE	0	-0.003	-0.005	23.332	-0.003	-0.003	0.000	0.000	0.000	0.000
28	A	754	MET	0	-0.029	-0.018	22.633	0.047	0.047	0.000	0.000	0.000	0.000
29	A	755	GLU	-1	-0.890	-0.936	22.830	0.179	0.179	0.000	0.000	0.000	0.000
30	A	756	PRO	0	-0.016	0.008	22.058	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	757	VAL	0	0.072	0.049	24.401	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	758	LYS	1	0.877	0.938	27.389	-0.159	-0.159	0.000	0.000	0.000	0.000
33	A	759	LYS	1	0.996	0.990	29.571	-0.057	-0.057	0.000	0.000	0.000	0.000
34	A	760	SER	0	-0.020	-0.012	32.795	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	761	GLU	-1	-0.935	-0.933	32.351	0.127	0.127	0.000	0.000	0.000	0.000
36	A	762	ALA	0	0.045	0.015	31.900	-0.001	-0.001	0.000	0.000	0.000	0.000
37	A	763	PRO	0	-0.029	-0.011	32.568	0.001	0.001	0.000	0.000	0.000	0.000
38	A	764	ASP	-1	-0.832	-0.904	33.621	0.070	0.070	0.000	0.000	0.000	0.000
39	A	765	TYR	0	0.049	0.029	25.689	0.002	0.002	0.000	0.000	0.000	0.000
40	A	766	TYR	0	-0.081	-0.079	24.905	0.003	0.003	0.000	0.000	0.000	0.000
41	A	767	GLU	-1	-0.878	-0.890	28.170	0.022	0.022	0.000	0.000	0.000	0.000
42	A	768	VAL	0	0.014	0.001	30.086	-0.003	-0.003	0.000	0.000	0.000	0.000
43	A	769	ILE	0	-0.031	-0.005	24.773	0.004	0.004	0.000	0.000	0.000	0.000
44	A	770	ARG	1	0.816	0.876	25.213	-0.024	-0.024	0.000	0.000	0.000	0.000
45	A	771	PHE	0	-0.026	-0.006	20.107	-0.012	-0.012	0.000	0.000	0.000	0.000
46	A	772	PRO	0	0.059	0.049	21.375	0.032	0.032	0.000	0.000	0.000	0.000
47	A	773	ILE	0	-0.064	-0.047	15.790	0.008	0.008	0.000	0.000	0.000	0.000
48	A	774	ASP	-1	-0.694	-0.811	19.008	0.252	0.252	0.000	0.000	0.000	0.000
49	A	775	LEU	0	0.078	0.010	18.199	0.048	0.048	0.000	0.000	0.000	0.000
50	A	776	LYS	1	0.818	0.929	17.950	-0.147	-0.147	0.000	0.000	0.000	0.000
51	A	777	THR	0	-0.017	-0.046	16.171	0.025	0.025	0.000	0.000	0.000	0.000
52	A	778	MET	0	-0.041	-0.011	13.398	0.008	0.008	0.000	0.000	0.000	0.000
53	A	779	THR	0	-0.017	-0.019	12.989	0.130	0.130	0.000	0.000	0.000	0.000
54	A	780	GLU	-1	-0.832	-0.904	13.435	0.280	0.280	0.000	0.000	0.000	0.000
55	A	781	ARG	1	0.880	0.951	10.798	-0.286	-0.286	0.000	0.000	0.000	0.000
56	A	782	LEU	0	-0.004	0.001	8.715	0.082	0.082	0.000	0.000	0.000	0.000
57	A	783	ARG	1	0.889	0.941	8.624	-0.244	-0.244	0.000	0.000	0.000	0.000
58	A	784	SER	0	-0.031	-0.026	9.786	-0.026	-0.026	0.000	0.000	0.000	0.000
59	A	785	ARG	1	0.826	0.894	4.284	-2.293	-2.135	-0.001	-0.015	-0.142	0.000
60	A	786	TYR	0	0.045	0.032	4.686	-0.330	-0.296	-0.001	-0.003	-0.029	0.000
61	A	787	TYR	0	-0.085	-0.073	6.398	-0.298	-0.298	0.000	0.000	0.000	0.000
62	A	788	VAL	0	0.051	0.014	2.266	1.148	1.702	3.338	-1.142	-2.749	0.000
63	A	789	THR	0	0.030	0.001	2.552	-3.403	-3.051	2.292	0.098	-2.742	-0.022
64	A	790	ARG	1	0.959	0.974	4.402	-1.851	-1.688	-0.001	-0.015	-0.147	0.000
65	A	791	LYS	1	0.984	0.985	6.495	-0.615	-0.615	0.000	0.000	0.000	0.000
66	A	792	LEU	0	0.011	0.025	6.492	-0.098	-0.098	0.000	0.000	0.000	0.000
67	A	793	PHE	0	0.046	0.020	9.277	-0.081	-0.081	0.000	0.000	0.000	0.000
68	A	794	VAL	0	0.014	-0.003	10.679	-0.139	-0.139	0.000	0.000	0.000	0.000
69	A	795	ALA	0	-0.018	-0.002	12.389	-0.095	-0.095	0.000	0.000	0.000	0.000
70	A	796	ASP	-1	-0.730	-0.824	13.605	0.315	0.315	0.000	0.000	0.000	0.000
71	A	797	LEU	0	0.026	0.010	15.083	-0.045	-0.045	0.000	0.000	0.000	0.000
72	A	798	GLN	0	-0.014	0.001	15.736	-0.057	-0.057	0.000	0.000	0.000	0.000
73	A	799	ARG	1	0.817	0.907	16.175	-0.286	-0.286	0.000	0.000	0.000	0.000
74	A	800	VAL	0	-0.007	0.006	19.075	-0.031	-0.031	0.000	0.000	0.000	0.000
75	A	801	ILE	0	-0.014	-0.003	21.598	-0.027	-0.027	0.000	0.000	0.000	0.000
76	A	802	ALA	0	-0.015	-0.006	22.741	-0.023	-0.023	0.000	0.000	0.000	0.000
77	A	803	ASN	0	-0.001	-0.018	22.187	-0.026	-0.026	0.000	0.000	0.000	0.000
78	A	804	CYS	0	-0.072	-0.010	25.600	-0.017	-0.017	0.000	0.000	0.000	0.000
79	A	805	ARG	1	0.808	0.836	25.440	-0.244	-0.244	0.000	0.000	0.000	0.000
80	A	806	GLU	-1	-0.941	-0.950	28.038	0.112	0.112	0.000	0.000	0.000	0.000
81	A	807	TYR	0	-0.065	-0.060	30.025	-0.009	-0.009	0.000	0.000	0.000	0.000
82	A	808	ASN	0	-0.052	-0.032	30.435	-0.012	-0.012	0.000	0.000	0.000	0.000
83	A	809	PRO	0	0.072	0.025	33.340	0.005	0.005	0.000	0.000	0.000	0.000
84	A	810	PRO	0	0.028	0.019	33.333	0.008	0.008	0.000	0.000	0.000	0.000
85	A	811	ASP	-1	-0.819	-0.879	33.788	0.143	0.143	0.000	0.000	0.000	0.000
86	A	812	SER	0	-0.005	-0.010	34.393	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	813	GLU	-1	-0.825	-0.919	34.526	0.164	0.164	0.000	0.000	0.000	0.000
88	A	814	TYR	0	-0.022	-0.029	30.749	0.016	0.016	0.000	0.000	0.000	0.000
89	A	815	CYS	0	0.021	0.018	30.155	0.021	0.021	0.000	0.000	0.000	0.000
90	A	816	ARG	1	0.773	0.876	30.345	-0.122	-0.122	0.000	0.000	0.000	0.000
91	A	817	CYS	0	-0.041	-0.021	29.308	0.015	0.015	0.000	0.000	0.000	0.000
92	A	818	ALA	0	0.031	0.004	26.294	0.023	0.023	0.000	0.000	0.000	0.000
93	A	819	SER	0	0.004	-0.011	25.733	0.025	0.025	0.000	0.000	0.000	0.000
94	A	820	ALA	0	-0.050	-0.014	26.869	0.015	0.015	0.000	0.000	0.000	0.000
95	A	821	LEU	0	-0.020	-0.009	22.252	0.023	0.023	0.000	0.000	0.000	0.000
96	A	822	GLU	-1	-0.781	-0.863	21.951	0.319	0.319	0.000	0.000	0.000	0.000
97	A	823	LYS	1	0.957	0.987	21.902	-0.218	-0.218	0.000	0.000	0.000	0.000
98	A	824	PHE	0	-0.012	-0.008	21.105	0.022	0.022	0.000	0.000	0.000	0.000
99	A	825	PHE	0	0.071	0.018	17.799	0.040	0.040	0.000	0.000	0.000	0.000
100	A	826	TYR	0	-0.009	-0.029	17.722	0.061	0.061	0.000	0.000	0.000	0.000
101	A	827	PHE	0	-0.034	-0.010	19.009	0.020	0.020	0.000	0.000	0.000	0.000
102	A	828	LYS	1	0.779	0.884	16.992	-0.483	-0.483	0.000	0.000	0.000	0.000
103	A	829	LEU	0	-0.008	-0.010	12.858	0.079	0.079	0.000	0.000	0.000	0.000
104	A	830	LYS	1	0.902	0.946	14.759	-0.386	-0.386	0.000	0.000	0.000	0.000
105	A	831	GLU	-1	-0.847	-0.900	17.185	0.539	0.539	0.000	0.000	0.000	0.000
106	A	832	GLY	0	0.019	0.007	13.687	-0.015	-0.015	0.000	0.000	0.000	0.000
107	A	833	GLY	0	-0.048	-0.022	12.628	0.083	0.083	0.000	0.000	0.000	0.000
108	A	834	LEU	0	-0.042	-0.013	9.043	0.147	0.147	0.000	0.000	0.000	0.000
109	A	835	ILE	0	-0.018	-0.012	10.971	0.068	0.068	0.000	0.000	0.000	0.000
110	A	836	ASP	-1	-0.851	-0.909	13.773	0.599	0.599	0.000	0.000	0.000	0.000
111	A	837	LYS	1	0.869	0.935	16.496	-0.650	-0.650	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:727:MET)